diff mcm_stitch.xml @ 0:c14690ec0c9f draft

"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mauve_contig_mover commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mcm_stitch.xml	Fri Jan 24 17:43:19 2020 -0500
@@ -0,0 +1,53 @@
+<tool id="mauve-contig-mover-stitch" name="Mauve Contig Mover - Stitch" version="1.0" profile="16.04">
+    <description>Concatenate multiple contigs, complementing reversed sequences and rewriting all feature coordinates</description>
+    <edam_topics>
+        <edam_topic>topic_0196</edam_topic>
+        <edam_topic>topic_0091</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3436</edam_operation>
+        <edam_operation>operation_0232</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="1.73">biopython</requirement>
+    </requirements>
+    <version_command><![CDATA[ $__tool_directory__/stitch.py -v ]]></version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        python $__tool_directory__/stitch.py
+        #if $seqid
+            -s '$seqid'
+        #else
+            -s '$draft.element_identifier.replace(" ", "_")'
+        #end if
+        $pad_len $draft $draft.ext
+        #if $contigs
+            $contigs
+        #end if
+        > $output
+    ]]></command>
+    <inputs>
+        <param name="draft" type="data" format="abi,abi-trim,ace,cif-atom,cif-seqres,clustal,embl,fasta,fasta-2line,fastq-sanger,fastq,fastq-solexa,fastq-illumina,genbank,gb,ig,imgt,nexus,pdb-seqres,pdb-atom,phd,phylip,pir,seqxml,sff,sff-trim,stockholm,swiss,tab,qual,uniprot-xml,gff3" label="Draft" />
+        <param name="contigs" type="data" format="tabular" label="Contigs" optional="true" help="Contigs output from Mauve Contig Mover" />
+        <param name="pad_len" type="integer" min="0" value="1000" label="Pad length" help="Specify the length of padding to put between contigs" />
+        <param name="seqid" type="text" value="" label="Stitched sequence ID" help="Specify an ID to use for the stitched record, the dataset ID is used otherwise" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="draft" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="draft" value="test-data/draft_bioperl.gbff" ftype="genbank" />
+            <param name="contigs" value="test-data/contig_order.tabular" ftype="tabular" />
+            <output name="output" checksum="sha256:08afe06a0f1eb96aa7f2a5b9e8a5ca15a4775c884f3144b6d82f2a0668cdb210" ftype="genbank" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Stitch contigs into a single contig.
+        Compliments reversed sequences and rewrites all feature coordinates.
+        For gankbank and embl, 'source' features are combined.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.3364789</citation>
+    </citations>
+</tool>